Advances in sequencing technologies over the last decade have led to the rapid production of large volumes of sequencing data for phylogenetic analyses. True phylogenomic studies are now possible, although remain constrained by both labour and cost. However, the availability of mitochondrial genome sequences is growing as a result of increased access to Next-Generation Sequencing platforms. The phylogenetic analysis of complete mitochondrial genomes is becoming the marker of choice within some taxa and the comparative analysis of entire mitogenome sequences has revealed new informative characters. Despite these technological improvements, assembling longer sequences, such as that of entire mitochondrial genomes, has not been straightforward. Very few large-scale studies exist, and have been primarily limited to nominally intra-specific datasets. This study explores the potential of amplifying, sequencing and assembling mitochondrial genomes from a diverse order; Araneae (spiders). To this end I have amplified spider mitogenomes via more traditional polymerase chain reaction (PCR) strategies and whole genome amplification (WGA) steps, in order to assess their utility in resolving phylogenetic in-congruence in hitherto understudied taxa. Whilst complete mitochondrial genomes were successfully sequenced, this research highlights the obstacles to the rapid amplification of large divergent mitogenomic datasets. However, the data generated from the study has been critical in elucidating the evolutionary history of the Araneae, the generation of robust phylogenetic hypotheses, and in dating the major radiations of extant spiders. To my knowledge this study represents the most complete comparative mitogenomic analysis within the Araneae to date, and provides a framework from which subsequent analyses can further delineate the evolutionary history of the order.